Análisis metagenómico y metatranscriptómico del microbioma bacteriano de Caligus rogercresseyi según el sexo y el desarrollo ontogenético.
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Date
2025
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Universidad de Concepción
Abstract
La caligidosis, causada por el piojo de mar Caligus rogercresseyi, representa uno de los principales desafíos sanitarios de la salmonicultura chilena, generando pérdidas productivas significativas y favoreciendo la aparición de infecciones secundarias en los peces. Aunque en los últimos años se ha avanzado en la caracterización taxonómica de la microbiota asociada a este parásito, su rol funcional ha sido escasamente abordado. Este estudio presenta la primera caracterización integrada del microbioma bacteriano de C. rogercresseyi, combinando secuenciación del gen 16S rRNA de longitud completa, predicción funcional y análisis metatranscriptómico bacteriano a partir de datos de RNA-seq del hospedador. Se analizó la microbiota de machos adultos, hembras adultas, intestinos y estadios infectivos (copepoditos). Los resultados evidenciaron una marcada influencia del sexo y del desarrollo ontogénico en la composición, la diversidad y la estructura funcional del microbioma. Las hembras presentaron una diversidad bacteriana significativamente mayor que la de los machos, mientras que los copepoditos exhibieron la mayor riqueza, posiblemente asociada a la exposición ambiental durante la fase planctónica. Se identificó un core microbioma conservado de 35 géneros compartidos entre todos los grupos, dominado por taxones marinos como Vibrio, Aliivibrio, Tenacibaculum y Sulfitobacter. La predicción funcional mediante PICRUSt2 reveló una clara diferenciación metabólica. La microbiota asociada a hembras mostró un enriquecimiento en rutas catabólicas y de generación de energía, incluyendo la β-oxidación de ácidos grasos y la glicólisis, lo cual es coherente con las altas demandas energéticas asociadas a la reproducción. En contraste, la microbiota de machos presentó una mayor representación de rutas biosintéticas, incluyendo la síntesis de aminoácidos, nucleótidos y lípidos, lo que sugiere un soporte metabólico orientado a la locomoción y al mantenimiento somático. Los análisis metatranscriptómicos confirmaron que estas funciones están expresadas activamente y revelaron una reorganización funcional a lo largo del desarrollo. La actividad bacteriana fue mínima en nauplios, disminuyó abruptamente en copepoditos y aumentó progresivamente desde chalimus hasta adultos, con una marcada diferenciación sexual. Los análisis KEGG y GO demostraron una microbiota altamente estructurada funcionalmente y acoplada a la fisiología del hospedador. En conjunto, los resultados apoyan un modelo de holobionte funcional para C. rogercresseyi, donde la microbiota emerge como componente activo y regulador de la biología del parásito, abriendo nuevas perspectivas para el control sanitario basado en la microbiota.
Sea lice infestation caused by Caligus rogercresseyi is a significant health challenge in salmon aquaculture in Chile, leading to substantial economic losses and increased vulnerability to secondary infections in farmed salmon. Although recent years have seen progress in the taxonomic identification of the microbiota associated with this ectoparasite, its functional role remains largely unknown. This study offers the first comprehensive characterization of the bacterial microbiome of C. rogercresseyi by integrating full-length 16S rRNA gene sequencing with functional prediction and bacterial metatranscriptomic analysis based on host RNA-seq data. Microbial communities were examined in adult males, adult females, intestinal samples, and infective copepodite stages. The results showed strong effects of both sex and ontogenetic development on microbiome composition, diversity, and functional structure. Females have significantly higher bacterial diversity than males, while copepodites showed the greatest overall richness, probably reflecting environmental acquisition during the planktonic stage. A conserved core microbiome comprising 35 genera was identified across all groups, dominated by marine-associated taxa including Vibrio, Aliivibrio, Tenacibaculum, and Sulfitobacter. Functional inference based on PICRUSt2 revealed clear metabolic specialization. The female-associated microbiota were enriched in catabolic and energy-generating pathways, such as fatty acid β- oxidation, glycolysis, and amino acid degradation, consistent with the energetic demands of reproduction. In contrast, the male-associated microbiota showed enrichment in anabolic pathways, including the biosynthesis of branched-chain amino acids, nucleotides, and lipids, suggesting metabolic support for mobility and somatic maintenance. Bacterial metatranscriptomic profiling confirmed that these predicted functions are actively expressed. Expression patterns varied markedly across development, with low activity in nauplius stages, a functional bottleneck at copepodite, and progressive metabolic activation in chalimus and adult stages, with strong sexual differentiation in adults. KEGG and Gene Ontology enrichment analyses further demonstrated a highly structured functional microbiome involved in metabolism, transport, energy production, and cellular regulation. Overall, these findings support a holobiont model for C. rogercresseyi, in which microbiota is an active and adaptable part of parasite biology. This study emphasizes microbiota as a potential target for innovative control strategies such as microbiome manipulation or anti-microbiota vaccines.
Sea lice infestation caused by Caligus rogercresseyi is a significant health challenge in salmon aquaculture in Chile, leading to substantial economic losses and increased vulnerability to secondary infections in farmed salmon. Although recent years have seen progress in the taxonomic identification of the microbiota associated with this ectoparasite, its functional role remains largely unknown. This study offers the first comprehensive characterization of the bacterial microbiome of C. rogercresseyi by integrating full-length 16S rRNA gene sequencing with functional prediction and bacterial metatranscriptomic analysis based on host RNA-seq data. Microbial communities were examined in adult males, adult females, intestinal samples, and infective copepodite stages. The results showed strong effects of both sex and ontogenetic development on microbiome composition, diversity, and functional structure. Females have significantly higher bacterial diversity than males, while copepodites showed the greatest overall richness, probably reflecting environmental acquisition during the planktonic stage. A conserved core microbiome comprising 35 genera was identified across all groups, dominated by marine-associated taxa including Vibrio, Aliivibrio, Tenacibaculum, and Sulfitobacter. Functional inference based on PICRUSt2 revealed clear metabolic specialization. The female-associated microbiota were enriched in catabolic and energy-generating pathways, such as fatty acid β- oxidation, glycolysis, and amino acid degradation, consistent with the energetic demands of reproduction. In contrast, the male-associated microbiota showed enrichment in anabolic pathways, including the biosynthesis of branched-chain amino acids, nucleotides, and lipids, suggesting metabolic support for mobility and somatic maintenance. Bacterial metatranscriptomic profiling confirmed that these predicted functions are actively expressed. Expression patterns varied markedly across development, with low activity in nauplius stages, a functional bottleneck at copepodite, and progressive metabolic activation in chalimus and adult stages, with strong sexual differentiation in adults. KEGG and Gene Ontology enrichment analyses further demonstrated a highly structured functional microbiome involved in metabolism, transport, energy production, and cellular regulation. Overall, these findings support a holobiont model for C. rogercresseyi, in which microbiota is an active and adaptable part of parasite biology. This study emphasizes microbiota as a potential target for innovative control strategies such as microbiome manipulation or anti-microbiota vaccines.
Description
Tesis presentada para optar al grado de Magíster en Ciencias con mención en Microbiología.
Keywords
Salmonicultura, Salmonidos Enfermedades, Microbioma gastrointestinal